GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

daptomycin   Click here for help

GtoPdb Ligand ID: 10904

Synonyms: Cubicin® | LY-146032 | LY146032
Approved drug
daptomycin is an approved drug (FDA (2003), EMA (2006))
Compound class: Synthetic organic
Comment: Daptomycin is a semi-synthetic cyclic lipopeptide antibacterial with broad-spectrum activity against Gram-positive bacteria. It is a bacterial metabolite that was isolated from Streptomyces roseosporus. Daptomycin rapidly depolarizes the bacterial cell membrane which disrupts DNA, RNA and protein synthesis and results in cell death.
This antibacterial was removed from the World Health Organization's List of Essential Medicines in 2019.
2D Structure
Click here for help

2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

✖
Hydrogen bond acceptors 42
Hydrogen bond donors 22
Rotatable bonds 39
Topological polar surface area 702.02
Molecular weight 1619.71
XLogP 1.92
No. Lipinski's rules broken 3

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
Click here for help

SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

✖
Canonical SMILES NCCC[C@@H]1NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](Cc2c[nH]c3c2cccc3)NC(=O)CCCCCCCCC)CC(=O)N)CC(=O)O)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC1=O)CC(=O)O)C)CC(=O)O)CO)[C@@H](CC(=O)O)C)CC(=O)c1ccccc1N
Isomeric SMILES NCCC[C@@H]1NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](Cc2c[nH]c3c2cccc3)NC(=O)CCCCCCCCC)CC(=O)N)CC(=O)O)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC1=O)CC(=O)O)C)CC(=O)O)CO)[C@@H](CC(=O)O)C)CC(=O)c1ccccc1N
InChI InChI=1S/C72H101N17O26/c1-5-6-7-8-9-10-11-22-53(93)81-44(25-38-31-76-42-20-15-13-17-39(38)42)66(108)84-45(27-52(75)92)67(109)86-48(30-59(102)103)68(110)89-61-37(4)115-72(114)49(26-51(91)40-18-12-14-19-41(40)74)87-71(113)60(35(2)24-56(96)97)88-69(111)50(34-90)82-55(95)32-77-63(105)46(28-57(98)99)83-62(104)36(3)79-65(107)47(29-58(100)101)85-64(106)43(21-16-23-73)80-54(94)33-78-70(61)112/h12-15,17-20,31,35-37,43-50,60-61,76,90H,5-11,16,21-30,32-34,73-74H2,1-4H3,(H2,75,92)(H,77,105)(H,78,112)(H,79,107)(H,80,94)(H,81,93)(H,82,95)(H,83,104)(H,84,108)(H,85,106)(H,86,109)(H,87,113)(H,88,111)(H,89,110)(H,96,97)(H,98,99)(H,100,101)(H,102,103)/t35-,36-,37-,43+,44+,45+,46+,47+,48+,49+,50-,60+,61+/m1/s1
InChI Key DOAKLVKFURWEDJ-RWDRXURGSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Synthetic organic
Approved drug? Yes. EU EMA (2006)  |  US FDA (2003)
International Nonproprietary Names Click here for help
INN number INN
6127 daptomycin
Synonyms Click here for help
Cubicin® | LY-146032 | LY146032
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Daptomycin (Cubicin)
Other databases
CAS Registry No. 103060-53-3 (source: WHO INN record)
ChEMBL Ligand CHEMBL387675
GtoPdb PubChem SID 405560345
PubChem CID 16134395
Search Google for chemical match using the InChIKey DOAKLVKFURWEDJ-RWDRXURGSA-N
Search Google for chemicals with the same backbone DOAKLVKFURWEDJ
Search PubMed clinical trials daptomycin
Search PubMed titles daptomycin
Search PubMed titles/abstracts daptomycin
UniChem Compound Search for chemical match using the InChIKey DOAKLVKFURWEDJ-RWDRXURGSA-N
UniChem Connectivity Search for chemical match using the InChIKey DOAKLVKFURWEDJ-RWDRXURGSA-N